Mapping and characterization of rust resistance genes Lr53 and Yr35 introgressed from Aegilops species

Key message The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Abstract Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the ph1b mutation obtained from the cross 98M71 × CSph1b, both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s00122-024-04616-x.


Fig. S2
Fig. S2 GISH images of the wheat line 98M71.Genomic DNA of Ae. longissima (S l S l ) and Ae.sharonensis (S sh S sh ) were labelled by the Atto550 NT labelling kit (red) and Atto488 NT labelling kit (green), respectively.Yellow arrows indicate the introgressed 6S chromosomes.

Fig. S5
Fig. S5 Transcript levels of (a) Ae.longissima.TL05.6S01G0003200.1 and (b) Ae.longissima.TL05.6S01G0009000.1 in mock-inoculated (green) and Pst-inoculated (blue) plants of 98M71 at 6 dpi.Seedlings of 98M71 was inoculated with Pst race CYR34 and mock inoculated in two independent growth chambers and leaf samples from different plants were collected at 6 dpi.Transcript levels were expressed as fold-Actin (n = 4).Error bars represent standard errors of the mean.*P < 0.05.

Fig. S6
Fig. S6 PCR amplification with the marker pku6B3127 and treatment of the amplified PCR products with restriction enzyme AvaI.The bands of 418-bp and 700-bp (red arrow) are present only in the introgression line 98M71 (TableS16).No amplification product was found in 11 tested T. turgidum (e.g.PI 221400, PI225332, and PI 254164).Treatment of the amplified PCR products with restriction enzyme AvaI generated a single 1118-bp (green arrow) band for the other tetraploid wheat accessions (e.g.CItr7687, CItr12213, and CItr12214).M, DNA ladders.

Fig. S7
Fig. S7 Fluorescence in situ hybridization (FISH) image of the resistant recombinant line C580.Probes pSc119.2(green), pTa535 (red), and pTa713 (yellow) were used for the hybridization experiments.Yellow arrows indicate the Oligo-pSc119.2signals in the telomeric region of the alien chromosome arm 6SS and white arrows represent the Oligo-pSc119.2signals in the telomeric region of wheat (CS) chromosome arm 6BL.

Fig. S8
Fig. S8 Infection types observed in the recombinant line C580 (progeny homozygous for the presence of the truncated alien segment), the original introgression line 98M71, and the recurrent parent CS (Chinese Spring).Plants were challenged with five Pt races (FHJR, PHQS, PHRT, PHTT, and THDB) and one Pst race (CYR34).